Bug fixes in GNOME are driven by volunteers, so if no one shows up to fix them after years, they are probably low priority and don't affect many people compared to the effort that it takes to fix them. Sorry, I don't know what else can be done about that, besides putting more strain on already strained open source maintainers. I don't know what you mean peer pressure to be a GNOME app. The file chooser and color chooser are unlikely to be changed unless somebody with a lot of UI/UX design experience volunteers to work on them, and makes them better in a way that benefits all GTK apps. The bugs with flatpak integration should probably be reported if they aren't already, the issue may be that some flatpak packages need to update their SDK version so they get a bug fixed version of GTK. Regarding your last sentence, issues in GNOME's wayland implementation won't affect users of other desktops.
Does that help? I don't think those are issues where you're being controlled into an unfixable situation, so I can try to help offer some solutions.
Does that help? I don't think those are issues where you're being controlled into an unfixable situation, so I can try to help offer some solutions.